We have a choice for buying at a good price a 6509E with SUP32 and 5 x 48 WS-X6148A-GE-45AF POE modules or a 4 x 2960S ( which then will be connected to existing 2 x 3560G 24 ports (for routing)). Both are (including 3 years maintenance) about the same price. What would be the better choice? According to the specs I read that SUP32 with the specific WS-X6148A boards has about 15 mpps performance with backplane speed of 32 Gbps whereas 2960S with flexstack has much higher mpps speed (up to 100 mpps as I understand) and much higher backplane speed, however this higher speed will probably not be effective when routing over copper etherchannel 4 Gbps to the existing 3560.
My preference would be the 6509E because of all the features, however not sure if we really need them, so key item is really performance.
What would the better choice be ?
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It's difficult to answer some of your questions, because as I've already noted, Cisco has NOT well documented how the FlexStack works.
For example, 3750 StackWise is documented (after the release of StackWise+) with putting everything on the ring, i.e. even traffic passing between two ports on the same switch. StackWise is also documented as the source switch removing traffic from the ring. StackWise+ changes how it operates in these two cases so it much better leverages its ring bandwidth, but how does FlexStack operate? I've seen it noted as it operates hop-by-hop, unlike StackWise, but what does this really mean?
When comparing the FlexStack dual 10 gig (duplex) links with the 6500's 16 gig (duplex) bus, does adding stack members effectively increase aggregate bandwidth within the stack vs. the 6500 bus? Does FlexStack add latency with each stack member and have higher latency vs. the 6500 bus? Again, I haven't seen this documented, and without knowing, how to we really determine which is likely to perform better in different situations?
It used to be the 2960S was only L2 but it now offers limited L3. How well does it perform L3 vs. a Sup32? Once again, I don't recall this being well documented.
Instead of looking at just "performance", you might want to also consider other things such as the Sup32 is now EOL. The 6500 requires a 2nd Sup for sup redundancy (while redundancy is inherent with the FlexStack). How do service contracts compare in cost?